Molecular Biotechnology最新文献

{"title":"Targeting PilA in Acinetobacter baumannii: A Computational Approach for Anti-Virulent Compound Discovery.","authors":"Mohanraj Gopikrishnan, George Priya C Doss","doi":"10.1007/s12033-024-01300-9","DOIUrl":"10.1007/s12033-024-01300-9","url":null,"abstract":"<p><p>Acinetobacter baumannii (A. baumannii) has emerged as a critical global pathogen due to its ability to acquire resistance traits. This bacterium exhibits two distinct forms of motility: twitching, mediated by type IV pili (T4P), and surface-associated motility, independent of appendages. T4P is crucial in various bacterial species, facilitating twitching motility, biofilm formation, and host-cell adhesion. The synthesis of T4P is a common feature among Gram-negative pathogens, particularly A. baumannii, suggesting that PilA could be a viable target for biofilm-related treatments. This study aims to develop drug molecules to mitigate A. baumannii virulence by targeting PilA. Using Schrodinger software, we screened 60,766 compounds from the CMNPD, ChemDiv, and Enamine antibacterial databases through high-throughput virtual screening. The top two compounds from each database, identified through extra precision (XP) mode, were subjected to further studies. Among the six compounds identified (CMNPD18469, CMNPD20698, Z2377302405, Z2378175729, N039-0021, and N098-0051), docking scores ranged from - 5.0 to - 7.5 kcal/mol. Subsequently, we conducted 300 ns molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis of the PilA-ligand complexes. Analysis of the simulation trajectories indicated structural stability and consistent behavior of the PilA-ligand complexes in a dynamic environment. Notably, the PilA-N098-0051 complex exhibited enhanced stability and robust binding interactions, underscoring its potential as a therapeutic agent. These findings suggest that the identified compounds, particularly N098-0051, hold promise as potent molecules targeting PilA, necessitating further validation through in vitro and in vivo studies.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3906-3921"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and Experimental Verification of PDK4 as a Potential Biomarker for Diagnosis and Treatment in Rheumatoid Arthritis.","authors":"Xifan Zheng, Junpu Huang, Jinzhi Meng, Hongtao Wang, Lingyun Chen, Jun Yao","doi":"10.1007/s12033-024-01297-1","DOIUrl":"10.1007/s12033-024-01297-1","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Rheumatoid arthritis (RA) is a chronic autoimmune disorder marked by sustained joint inflammation, with an etiology that remains elusive. Achieving an early and precise diagnosis poses significant challenges. This study aims to elucidate the molecular pathways involved in RA pathogenesis by screening genes associated with its occurrence, analyzing the related molecular activities, and ultimately developing more effective molecular-level treatments for RA.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Microarray expression profiling datasets GSE1919, GSE10500, GSE15573, GSE77298, GSE206848, and GSE236924 were sourced from the Gene Expression Omnibus (GEO) database. Samples were divided into experimental (RA) and control (normal) groups. Differentially expressed genes (DEGs) were identified using R software packages such as limma, glmnet, e1071 as well as randomForest. Cross-validation of DEGs was conducted using lasso regression and the random forest (RF) algorithm in R software to pinpoint intersecting genes that met the criteria. Among these, one gene was selected as the target for correlation analysis to identify DEGs related to the target gene. Enrichment analysis utilized the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases and Gene Ontology (GO) data. Gene Set Enrichment Analysis (GSEA) was performed to compare the expression levels of the target gene (PDK4) across various biological pathways and functions in groups with high and low expression. The relationship between target gene expression levels and cellular immune function was assessed using the immune function score technique. The discrepancy in immune cell distribution between the control and experimental groups, as well as their correlation with target gene expression levels, was elucidated using CIBERSORT. The relationships between mRNA, lncRNA, and miRNA were depicted in the ceRNA regulation network. The expression levels of the target gene were validated using Western blot and qRT-PCR.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;In this study, six intersecting genes meeting the criteria were identified through cross-validation, and PDK4 was chosen as the target gene for further investigation. Functional analysis using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) revealed that PDK4-associated DEGs are primarily enriched in the PPAR signaling pathway, thereby regulating synovial cell proliferation and migration, ultimately influencing the onset and progression of rheumatoid arthritis (RA). Immune infiltration analysis suggested that eosinophil quantity may influence the progression of RA. Experimental results from PCR and Western blot confirmed the downregulation of PDK4 in the RA group.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The significant downregulation of PDK4 expression in patients diagnosed with rheumatoid arthritis (RA) was confirmed. PDK4 may function as a novel regulatory factor in the onset an","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3975-3992"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Targeting miR-146b-5p to Regulate KDM6B Expression Aggravates Bronchopulmonary Dysplasia.","authors":"YunFeng Long, Yong Luo, Liu Hu, Hong Liao, Jin Liu","doi":"10.1007/s12033-024-01302-7","DOIUrl":"10.1007/s12033-024-01302-7","url":null,"abstract":"","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"4010"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lag Plot: A Novel Method to Determine Viable Bacterial Cell Number via a Single OD Measurement.","authors":"Alireza Ebrahiminezhad, Abdolreza Karami, Zeinab Karimi, Mohammad Kargar, Ahmad Vaez, Aydin Berenjian","doi":"10.1007/s12033-024-01295-3","DOIUrl":"10.1007/s12033-024-01295-3","url":null,"abstract":"<p><p>Bactericidal activity is a valuable parameter which is considered and measured for antimicrobial compounds. The available standard protocol to evaluate bactericidal activity is based on the direct colony count. Colony counting requires serial dilution, plating, overnight incubation, and direct counting, which is time-and labor-intensive. In regard to eliminate direct plate count, novel techniques were developed based on the real-time growth monitoring which can come with some limitations and drawbacks. These drawbacks encourage us to develop a novel technique with simple procedure to determine viable bacterial cell count. In this procedure, real-time growth monitoring is not required. In fact, after an incubation time, the number of viable bacteria can be determined with a single OD measurement and through an equation. In this regard, four standard bacterial strains, including Staphylococcus aureus (ATCC 25923), Escherichia coli (ATCC 25922), Pseudomonas aeruginosa (ATCC 27853), and Bacillus subtilis (ATCC 23857), were cultured with descending inoculum densities (1.5 × 10⁷ to 15 CFU/mL) and growth curves were drawn. As expected, growth in the samples with lower inoculum densities recorded with longer lag phase. Also, a direct relation was observed between the recorded turbidities and initial cell counts. A logarithmic curve (lag plot) was obtained by plotting the OD, after 12-18 h incubation, against initial cell counts. In all examined strains, R² was calculated in the range of 0.96-0.99 which is acceptable value for coefficient of determination. Equation corresponding to the lag plot was obtained and called lag equation. This equation is applicable to calculate the number of viable cells in unknown samples simply by inoculation, incubation, and single OD measurement. Developed technique can be introduced as a simple substitution for labor- and time-intensive direct colony counting.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3849-3857"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in Metabolic Engineering for the Accumulation of Astaxanthin Biosynthesis.","authors":"Bingxin Yu, Tianyue Ma, Maryam Nawaz, Hailong Chen, Heng Zheng","doi":"10.1007/s12033-024-01289-1","DOIUrl":"10.1007/s12033-024-01289-1","url":null,"abstract":"<p><p>Astaxanthin, a lipophilic carotenoid renowned for its strong antioxidant activity, holds significant commercial value across industries such as feed, food, and cosmetics. Although astaxanthin can be synthesized through chemical methods, it may contain toxic by-products in the synthesized astaxanthin, limiting its application in medicine or functional food. Natural astaxanthin can be extracted from algae, however, the cultivation cycle of algae is relatively longer compared to microorganisms. With the advancement of synthetic biology and metabolic engineering, the method of microbial fermentation has emerged as a promising strategy for the large-scale production of astaxanthin. This article provides a comprehensive overview of the research progress in astaxanthin biosynthesis, highlighting the use of the natural host Xanthophyllomyces dendrorhous, and the heterologous hosts Yarrowia lipolytica and Saccharomyces cerevisiae. Additionally, future research prospects are also discussed.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3769-3785"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Large Clostridial Toxins: A Brief Review and Insights into Antigen Design for Veterinary Vaccine Development.","authors":"Rafael Rodrigues Rodrigues, Mariliana Luiza Ferreira Alves, Miguel Andrade Bilhalva, Frederico Schmitt Kremer, Clóvis Moreira Junior, Marcos Roberto Alves Ferreira, Cleideanny Cancela Galvão, Pedro Henrique Dala Nora Quatrin, Fabricio Rochedo Conceição","doi":"10.1007/s12033-024-01303-6","DOIUrl":"10.1007/s12033-024-01303-6","url":null,"abstract":"<p><p>The group of large clostridial toxins (LCTs) includes toxins A (TcdA) and B (TcdB) from Clostridioides difficile, hemorrhagic and lethal toxins from Paeniclostridium sordellii, alpha toxin from Clostridium novyi (TcnA), and cytotoxin from Clostridium perfringens. These toxins are associated with severe pathologies in livestock, including gas gangrene (P. sordellii and C. novyi), infectious necrotic hepatitis (C. novyi), avian necrotic enteritis (C. perfringens), and enterocolitis (C. difficile). Immunoprophylaxis is crucial for controlling these diseases, but traditional vaccines face production challenges, such as labor-intensive processes, and often exhibit low immunogenicity. This has led to increased interest in recombinant vaccines. While TcdA and TcdB are well-studied for human immunization, other LCTs remain poorly characterized and require further investigation. Therefore, this study emphasizes the importance of understanding lesser-explored toxins and proposes using immunoinformatics to identify their immunodominant regions. By mapping these regions using silico tools and considering their homology with TcdA and TcdB, the study aims to guide future research in veterinary vaccinology. It also explores alternatives to overcome the limitations of conventional and recombinant vaccines, offering guidelines for developing more effective vaccination strategies against severe infections in animals.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3823-3839"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the Role of OsHDT701 and Other Blast-Associated Negative Regulatory Genes in Indica Rice Cultivar Ranjit Using Combined Wet Lab and Computational Approaches.","authors":"Yogita N Sarki, Hidam Bishworjit Singh, Ajay Kumar Keot, Riwandahun Marwein, Dhanawantari L Singha, Budheswar Dehury, Channakeshavaiah Chikkaputtaiah","doi":"10.1007/s12033-024-01310-7","DOIUrl":"10.1007/s12033-024-01310-7","url":null,"abstract":"<p><p>Rice blast, caused by Magnaporthe oryzae, severely impacts global rice production. Understanding the role of the host's blast negative regulatory genes is crucial for combating this disease. We studied the expression of seven rice blast negative regulatory genes (previously characterized in ssp. japonica) in susceptible (Ranjit and Mahsuri) and tolerant/resistant (Shahsarang 1 and IR64) indica rice cultivars during M. oryzae infection. The selected genes showed differential expression patterns, with OsHDT701 (histone H4 deacetylase) downregulated in tolerant/resistant and upregulated in susceptible cultivars. Promoter analysis of OsHDT701 in cv. Ranjit revealed biotic stress-responsive and M. oryzae effector binding motifs (MoHTR2 and MoSPAB1). Protein-DNA docking showed an interaction for both the effectors and promoter sequences. Furthermore, a strong interaction between the OsERF922 transcription factor (a negative regulator of rice blast) and GCC box at the promoter suggests OsERF922-mediated regulation of OsHDT701. Next, a comparative analysis of ssp. japonica (Nipponbare) OsHDT701 CDS to 11 indica rice cultivars, including Ranjit, detected an SNP (T-A) at position 591. Moreover, the structure modeling and protein-protein interaction reveal that OsHDT701 may form a complex with other histone deacetylases to regulate defense-related gene expression. Taken together, our study unveils new possibilities for OsHDT701 regulation mechanisms during M. oryzae infection.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3993-4009"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-Cas9: Unraveling Genetic Secrets to Enhance Floral and Fruit Traits in Tomato.","authors":"S Bhoomika, Shubham Rajaram Salunkhe, A R Sakthi, T Saraswathi, S Manonmani, M Raveendran, M Sudha","doi":"10.1007/s12033-024-01290-8","DOIUrl":"10.1007/s12033-024-01290-8","url":null,"abstract":"<p><p>Tomato, a globally consumed vegetable, possesses vast genetic diversity, making it suitable for genetic manipulation using various genetic improvement techniques. Tomatoes are grown extensively for their market value and health benefits, primarily contributed by enhanced yield and nutritional value respectively, influenced by floral and fruit traits. Floral morphology is maintained by genes involved in meristem size control, regulation of inflorescence transition, and pollen development. SP (SELF-PRUNING) and SP5G (SELF-PRUNING 5G) determine growth habit and flowering time. RIN (RIPENING INHIBITOR) and PG (POLYGALACTURONASE) are responsible for the shelf life of fruits. In addition to this, nutrition-enriched tomatoes have been developed in recent times. In this review, we comprehensively discuss the major genes influencing floral morphology, flowering time, fruit size, fruit shape, shelf life, and nutritional value, ultimately resulting in enhanced yield. Additionally, we address the advances in CRISPR/Cas9 applied for the genetic improvement of tomatoes along with prospects of areas in which research development in terms of tomato genetic improvement has to be advanced.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3786-3799"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scaffold Hopping Method for Design and Development of Potential Allosteric AKT Inhibitors.","authors":"Alireza Poustforoosh","doi":"10.1007/s12033-024-01307-2","DOIUrl":"10.1007/s12033-024-01307-2","url":null,"abstract":"<p><p>Targeting AKT is a practical strategy for cancer therapy in many cancer types. Targeted inhibitors of AKT are attractive solutions for inhibiting the interconnected signaling pathways, like PI3K/Akt/mTOR. Allosteric inhibitors are more desirable among different classes of AKT inhibitors as they could be more specific with fewer off-target proteins. In this study, a ligand/structure-based pipeline was developed to design new allosteric AKT inhibitors by employing the core hopping method. Triciribine, a traditional allosteric AKT inhibitor was used as the template, and the FDA-approved kinase inhibitors for cancer treatment were considered as the cores. The allosteric site in the crystal structure of AKT1 was used to screen the designed compounds. The results were further evaluated using molecular docking, ADME/T analysis, molecular dynamics (MD) simulation, and binding free energy calculations. The outcomes introduced 24 newly designed inhibitors, amongst which three compounds C6, C20, and C16 showed remarkable binding affinity to AKT1. While the docking scores for triciribine was around - 8.6 kcal/mol, the docking scores of these compounds were about - 11 to - 13 kcal/mol. The MD results indicated that designed compounds target the essential residues of the PH domain and kinase domain of AKT, such as Trp80, Thr211, Tyr272, Asp274, and Asp292. Scaffold hopping is a tremendous tool for designing novel anti-cancer agents by improving already known and potential drug compounds. The designed compounds are worth to be examined by experimental investigation in vitro and in vivo.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3960-3974"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression Profile and Prognostic Significance of Pivotal Regulators for N7-Methylguanosine Methylation in Diffuse Large B-Cell Lymphoma.","authors":"Cong Wang, Ran Kong, Guangcai Zhong, Peipei Li, Na Wang, Ganyu Feng, Mei Ding, Xiangxiang Zhou","doi":"10.1007/s12033-024-01264-w","DOIUrl":"10.1007/s12033-024-01264-w","url":null,"abstract":"<p><p>N7-methylguanosine (m7G) occurs by adding a methyl group to the N7 atom of the RNA guanine. Emerging evidence suggests that m7G modification has emerged as a crucial regulator of tumorigenesis, progression, invasion, and metastasis in multiple cancers. Nevertheless, the utility of m7G modification in diffuse large B-cell lymphoma (DLBCL) remains undefined, notably the interaction with the tumor microenvironment (TME). Here, we aimed to identify the expression profile of m7G regulators in DLBCL, construct a novel risk model, and explore their connection with TME. We initially investigated the difference and correlation in m7G regulators' expression in normal and tumor groups, classified patients by consistent clustering analysis, investigated the functional and prognostic significance of the resulting subtypes, and identified prognosis-associated genes by one-way Cox and least absolute shrinkage and selection operator (LASSO) regression calculations, and constructed a risk model. Further analysis showed that correlation among immune cell infiltration with m7G risk score and determined that it impacts the prognosis of DLBCL patients. Our research demonstrated the relevance of m7G regulators to DLBCL prognosis, providing theoretical support for precise prognostic stratification and immunotherapeutic assessment in DLBCL.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"3930-3945"},"PeriodicalIF":2.5,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}